The overriding purpose of the Functional Genomics Core (FGC) is to provide to the Scripps NeuroAIDS Preclinical Studies (SNAPS) Center Investigators relevant state of the art technologies and assays for gene function analysis. The SNAPS center Investigators recognize there is likely not to be a single mechanistic cause of CNS dysfunction in NeuroAIDS and therefore have evolved combinatorial and multi- disciplinary research approaches to the examination of basic mechanisms in understanding the pathogenesis of HIV infection in the CNS. The FGC aims to compliment and extend the synergy of our research efforts in this multi-disciplinary research setting, to identify and understand the function of key molecular genetic alterations in the CNS in response to viral and/or host response related perturbations relative to the various neuroAIDS models. In effect, the FGC will provide services and support that facilitate the application of functional genomics to advance our understanding of the pathogenesis of neuroAIDS. The overall specific aims of the FGC are: (1) To provide high-density gene expression analysis using in-house constructed DNA microarrays. In addition, support and advice will be given to Investigators concerning the possible application in their studies of commercially available (e.g. Affymetrix and Incyte) microarray services. (2) To provide multi-probe RNase protection assays to study in more specific and quantitative detail the regulation of candidate genes identified by DNA microarray analysis. (3) To perform single and dual label in situ hybridization procedures for the anatomic and cellular localization of expressed candidate genes. (4) To continually enhance the utility, relevance and ensure services remain state of the art, the FGC will undertake to generate and add new gene probes to the existing DNA microarray, RNase protection and in situ hybridization assays. (5) To provide support to CSPAR Investigators in all aspects of functional genomics. (7) To interact closely with the Administrative Core and other research cores and Investigators to fulfill the obligations of the FGC in the education, outreach and collaborative activities of the CSPAR center.